BrAD-seq: Breath Adapter Directional sequencing: a streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA library construction
Identifieur interne : 000058 ( Pmc/Curation ); précédent : 000057; suivant : 000059BrAD-seq: Breath Adapter Directional sequencing: a streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA library construction
Auteurs : Brad T. Townsley ; Michael F. Covington ; Yasunori Ichihashi ; Kristina Zumstein ; Neelima R. SinhaSource :
- Frontiers in Plant Science [ 1664-462X ] ; 2015.
Abstract
Next Generation Sequencing (NGS) is driving rapid advancement in biological understanding and RNA-sequencing (RNA-seq) has become an indispensable tool for biology and medicine. There is a growing need for access to these technologies although preparation of NGS libraries remains a bottleneck to wider adoption. Here we report a novel method for the production of strand specific RNA-seq libraries utilizing the terminal breathing of double-stranded cDNA to capture and incorporate a sequencing adapter. Breath Adapter Directional sequencing (BrAD-seq) reduces sample handling and requires far fewer enzymatic steps than most available methods to produce high quality strand-specific RNA-seq libraries. The method we present is optimized for 3-prime Digital Gene Expression (DGE) libraries and can easily extend to full transcript coverage shotgun (SHO) type strand-specific libraries and is modularized to accommodate a diversity of RNA and DNA input materials. BrAD-seq offers a highly streamlined and inexpensive option for RNA-seq libraries.
Url:
DOI: 10.3389/fpls.2015.00366
PubMed: 26052336
PubMed Central: 4441129
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Sinha</name></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">26052336</idno><idno type="pmc">4441129</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4441129</idno><idno type="RBID">PMC:4441129</idno><idno type="doi">10.3389/fpls.2015.00366</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000058</idno><idno type="wicri:Area/Pmc/Curation">000058</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">BrAD-seq: Breath Adapter Directional sequencing: a streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA library construction</title><author><name sortKey="Townsley, Brad T" sort="Townsley, Brad T" uniqKey="Townsley B" first="Brad T." last="Townsley">Brad T. Townsley</name></author><author><name sortKey="Covington, Michael F" sort="Covington, Michael F" uniqKey="Covington M" first="Michael F." last="Covington">Michael F. Covington</name></author><author><name sortKey="Ichihashi, Yasunori" sort="Ichihashi, Yasunori" uniqKey="Ichihashi Y" first="Yasunori" last="Ichihashi">Yasunori Ichihashi</name></author><author><name sortKey="Zumstein, Kristina" sort="Zumstein, Kristina" uniqKey="Zumstein K" first="Kristina" last="Zumstein">Kristina Zumstein</name></author><author><name sortKey="Sinha, Neelima R" sort="Sinha, Neelima R" uniqKey="Sinha N" first="Neelima R." last="Sinha">Neelima R. Sinha</name></author></analytic><series><title level="j">Frontiers in Plant Science</title><idno type="eISSN">1664-462X</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Next Generation Sequencing (NGS) is driving rapid advancement in biological understanding and RNA-sequencing (RNA-seq) has become an indispensable tool for biology and medicine. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Front Plant Sci</journal-id><journal-id journal-id-type="iso-abbrev">Front Plant Sci</journal-id><journal-id journal-id-type="publisher-id">Front. Plant Sci.</journal-id><journal-title-group><journal-title>Frontiers in Plant Science</journal-title></journal-title-group><issn pub-type="epub">1664-462X</issn><publisher><publisher-name>Frontiers Media S.A.</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">26052336</article-id><article-id pub-id-type="pmc">4441129</article-id><article-id pub-id-type="doi">10.3389/fpls.2015.00366</article-id><article-categories><subj-group subj-group-type="heading"><subject>Plant Science</subject><subj-group><subject>Methods</subject></subj-group></subj-group></article-categories><title-group><article-title>BrAD-seq: Breath Adapter Directional sequencing: a streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA library construction</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Townsley</surname><given-names>Brad T.</given-names></name><uri xlink:type="simple" xlink:href="http://community.frontiersin.org/people/u/86855"></uri></contrib><contrib contrib-type="author"><name><surname>Covington</surname><given-names>Michael F.</given-names></name><uri xlink:type="simple" xlink:href="http://community.frontiersin.org/people/u/223255"></uri></contrib><contrib contrib-type="author"><name><surname>Ichihashi</surname><given-names>Yasunori</given-names></name><xref ref-type="author-notes" rid="fn003"><sup>†</sup></xref><uri xlink:type="simple" xlink:href="http://community.frontiersin.org/people/u/65004"></uri></contrib><contrib contrib-type="author"><name><surname>Zumstein</surname><given-names>Kristina</given-names></name><uri xlink:type="simple" xlink:href="http://community.frontiersin.org/people/u/237914"></uri></contrib><contrib contrib-type="author"><name><surname>Sinha</surname><given-names>Neelima R.</given-names></name><xref ref-type="author-notes" rid="fn001"><sup>*</sup></xref><uri xlink:type="simple" xlink:href="http://community.frontiersin.org/people/u/25789"></uri></contrib></contrib-group><aff><institution>Department of Plant Biology, University of California, Davis</institution><country>Davis, CA, USA</country></aff><author-notes><fn fn-type="edited-by"><p>Edited by: Stefan De Folter, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico</p></fn><fn fn-type="edited-by"><p>Reviewed by: Kerstin Kaufmann, Potsdam University, Germany; Vagner Benedito, West Virginia University, USA</p></fn><corresp id="fn001">*Correspondence: Neelima R. Sinha, Department of Plant Biology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA <email xlink:type="simple">nrsinha@ucdavis.edu</email></corresp><fn fn-type="other" id="fn002"><p>This article was submitted to Plant Evolution and Development, a section of the journal Frontiers in Plant Science</p></fn><fn fn-type="present-address" id="fn003"><p>†Present Address: Yasunori Ichihashi, RIKEN Center for Sustainable Resource Science, Yokohama, Japan</p></fn></author-notes><pub-date pub-type="epub"><day>22</day><month>5</month><year>2015</year></pub-date><pub-date pub-type="collection"><year>2015</year></pub-date><volume>6</volume><elocation-id>366</elocation-id><history><date date-type="received"><day>11</day><month>3</month><year>2015</year></date><date date-type="accepted"><day>08</day><month>5</month><year>2015</year></date></history><permissions><copyright-statement>Copyright © 2015 Townsley, Covington, Ichihashi, Zumstein and Sinha.</copyright-statement><copyright-year>2015</copyright-year><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.</license-p></license></permissions><abstract><p>Next Generation Sequencing (NGS) is driving rapid advancement in biological understanding and RNA-sequencing (RNA-seq) has become an indispensable tool for biology and medicine. There is a growing need for access to these technologies although preparation of NGS libraries remains a bottleneck to wider adoption. Here we report a novel method for the production of strand specific RNA-seq libraries utilizing the terminal breathing of double-stranded cDNA to capture and incorporate a sequencing adapter. Breath Adapter Directional sequencing (BrAD-seq) reduces sample handling and requires far fewer enzymatic steps than most available methods to produce high quality strand-specific RNA-seq libraries. The method we present is optimized for 3-prime Digital Gene Expression (DGE) libraries and can easily extend to full transcript coverage shotgun (SHO) type strand-specific libraries and is modularized to accommodate a diversity of RNA and DNA input materials. BrAD-seq offers a highly streamlined and inexpensive option for RNA-seq libraries.</p></abstract><kwd-group><kwd>strand-specific sequencing</kwd><kwd>NGS</kwd><kwd>Illumina</kwd><kwd>RNA-seq libraries</kwd><kwd>Bioinformatics</kwd><kwd>BrAD-seq</kwd></kwd-group><counts><fig-count count="6"></fig-count><table-count count="3"></table-count><equation-count count="0"></equation-count><ref-count count="16"></ref-count><page-count count="11"></page-count><word-count count="7019"></word-count></counts></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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